At2g14340.1/PDB
&&&&&&&&&&&&&&&&&&&& BEGIN /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues &&&&&&&&&&&&&&&&&&&& Successfully read 2 file paths from WYRM_file_paths.txt generic_input /usr/local/www/html/proteins/workspace/ generic_output /usr/local/www/html/proteins/htdocs/results/ Sequence file type = 3 Sequence type = 3 Got here 1 Got here 2 Got here 3 Sequence 1 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Sequence 2 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Got here 3 Got here 4 Read 2 amino_acid sequences from PIR Sequence file /usr/local/www/html/proteins/workspace/At2g14340-1zgmA.pir.txt Assigned types to 220 residues in Sequence 2-14340, 17 remain unknown Assigned types to 189 residues in Sequence 1zgmA, 48 remain unknown Successfully read 576 entries for residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat Read the residue match scoring matrix /usr/local/www/html/proteins/workspace/BLOSUM62.dat Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 55 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 92 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 93 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 94 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 95 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 135 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 136 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 137 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 138 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 139 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 140 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 141 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 171 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 172 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 176 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 177 All residues are positively and negatively charged Error in function WYRM_analyze_conservation_in_sequence_alignment() Path index 183 All residues are positively and negatively charged Translated sequence file At2g14340-1zgmA.pir.txt into sequence alignment. >1ZGM=2FNO.pdb Made from 3517 ATOM records in 1ZGM=2FNO.pdb HHHEDGNTFDLYYWPVPFRGQLIRGILAHCGCSWDEHDVDAIEGLDCGAE KQPVAFGPPVLIDRERNFAISQPAIAIYLGERLDILPATVEGRTLSAKIV NDANDVLDELTLNGGREWTPEKWQEFVPRLQKWIRIFADTGARNGLSAAS GFLGTEKIGVADIVTAILWTTVADRFPAIKGIIEDTSPIIWGLSRRVVAT APLAALNSKSFEEYGNAYCGGEIEKSLRKVASDGNTFDLYYWPVPFRGQL IRGILAHCGCSWDEHDVDAIEGLDCGAEKQPVAFGPPVLIDRERNFAISQ PAIAIYLGERLDILPATVEGRTLSAKIVNDANDVLDELTLNGGREWTPEK WQEFVPRLQKWIRIFADTGARNGLSAASGFLGTEKIGVADIVTAILWTTV ADRFPAIKGIIEDTSPIIWGLSRRVVATAPLAALNSKSFEEYGNAYCGGE IEKSLRKVAS Best alignment: 1ZGM=2FNO.pdb 2 HHEDG-NTFDLYYWPVPFRGQLIRGILAHCGCSWDEHDVDAIEGL-DCGA 49 H EDG NTFDLYYWPVPFRGQLIRGILAHCGCSWDEHDVDAIEGL DCGA 1zgmA 1 HMEDGMNTFDLYYWPVPFRGQLIRGILAHCGCSWDEHXVDAIEGLMDCGA 50 1ZGM=2FNO.pdb 50 EKQPVAF-GPPVLIDRERNFAIS-QPAIAIYLGERLDILPATVEGRTLSA 97 EKQPVAF GPPVLIDRERNFAIS QPAIAIYLGERLDILPATVEGRTLSA 1zgmA 51 EKQPVAFMGPPVLIDRERNFAISQXXXXAIYLGERLDILPATVEGRTLSA 100 1ZGM=2FNO.pdb 98 KIVNDANDVLDELTLN-GGREWTPEKWQEFVPRLQKWIRIFADTGARNGL 146 KIVNDANDVLDELTLN GGREWTPEKWQEFVPRLQKWIRIFADTGARNGL 1zgmA 101 KIVNDANDVLDELTLNGXXXXXXXEKWQEFVPRLQKWIRIFADTGARNGL 150 1ZGM=2FNO.pdb 147 SAASGF-LGTEKIGVADIVTAILWTTVADRFPAIKGIIEDTSPIIWGLSR 195 SAASGF LGTEKIGVADIVTAILWTTVADRFPAIKGIIEDTSPIIWGLSR 1zgmA 151 SAAXXFMLXXEKIGVXDIVTAILWTTVADRFPAIKGIIEDTSPIIWGLSR 200 1ZGM=2FNO.pdb 196 RVVATA 201 RVVATA 1zgmA 201 RVVATA 206 Highlighted IDENTICAL residue ILE 22 index1 23 path 40 %Seq 100.00 Highlighted IDENTICAL residue ILE 25 index1 26 path 43 %Seq 100.00 Highlighted IDENTICAL residue HIS 28 index1 29 path 46 %Seq 100.00 Highlighted IDENTICAL residue GLY 30 index1 31 path 48 %Seq 100.00 Highlighted IDENTICAL residue PRO 53 index1 53 path 71 %Seq 100.00 Highlighted IDENTICAL residue ARG 67 index1 66 path 85 %Seq 100.00 Highlighted IDENTICAL residue PHE 69 index1 68 path 87 %Seq 100.00 Highlighted IDENTICAL residue ILE 79 index1 77 path 97 %Seq 100.00 Highlighted IDENTICAL residue GLY 82 index1 80 path 100 %Seq 100.00 Highlighted IDENTICAL residue GLU 93 index1 91 path 111 %Seq 100.00 Highlighted IDENTICAL residue LEU 133 index1 130 path 151 %Seq 100.00 Highlighted IDENTICAL residue ARG 138 index1 135 path 156 %Seq 100.00 Highlighted IDENTICAL residue ILE 162 index1 158 path 180 %Seq 100.00 Highlighted IDENTICAL residue PHE 180 index1 176 path 202 %Seq 100.00 Highlighted IDENTICAL residue ILE 186 index1 182 path 208 %Seq 100.00 Highlighted IDENTICAL residue GLU 188 index1 184 path 210 %Seq 100.00 Highlighted IDENTICAL residue ASP 189 index1 185 path 211 %Seq 100.00 Highlighted IDENTICAL residue PRO 192 index1 188 path 214 %Seq 100.00 Highlighted IDENTICAL residue ARG 200 index1 196 path 222 %Seq 100.00 Highlighted IDENTICAL residue VAL 201 index1 197 path 223 %Seq 100.00 Highlighted 20 residues for visualization Wrote PyMOL macro into file /usr/local/www/html/proteins/htdocs/results/At2g14340-1zgmA.pir.txt.1ZGM=2FNO.pdb.conservation.pml The program /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues At2g14340-1zgmA.pir.txt PIR amino_acid 1ZGM=2FNO.pdb _ 100.0 BLOSUM62.dat completed successfully. @@@@@@@@@@@@@@@@@@@@ END /usr/local/www/html/proteins/Compiled_Programs/WYRM/PyMOL_highlight_conserved_residues @@@@@@@@@@@@@@@@@@@@